Scale adjust a cDNA Microarray Object

Description

This function loads a maigesRaw or maiges object and scale adjust (normalise between arrays) the data using functions from limma package.

Usage

normScaleLimma(obj=NULL, ...)

Arguments

Details

This function for scale adjustment is entirely based on function normalizeBetweenArrays from limma package. See the help page for this function to see how to set the parameters. Pay attention to the 'vsn' method of scale adjustment, that must be used alone.

Value

This function returns a maiges object.

Author(s)

Gustavo H. Esteves <gesteves@vision.ime.usp.br>

See Also

normalizeBetweenArrays from limma package.

Examples

## Loading the dataset
data(gastro)

## Doing the scale adjustment from median-absolute-value method (from
## limma)
gastro.norm = normScaleLimma(gastro.norm, method="scale")
boxplot(gastro.norm) ## To see the efect of adjustment

## To do VSN scale adjustment (from vsn package) use the command. Be
## carefull that this method adjust the variance along A values and not
## between chips!!
gastro.norm = normScaleLimma(gastro.raw2, method="vsn")
boxplot(gastro.norm) ## See the effect

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(maigesPack)
Loading required package: convert
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: marray
Loading required package: graph
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/maigesPack/normScaleLimma.Rd_%03d_medium.png", width=480, height=480)
> ### Name: normScaleLimma
> ### Title: Scale adjust a cDNA Microarray Object
> ### Aliases: normScaleLimma
> ### Keywords: classes
> 
> ### ** Examples
> 
> ## Loading the dataset
> data(gastro)
> 
> ## Doing the scale adjustment from median-absolute-value method (from
> ## limma)
> gastro.norm = normScaleLimma(gastro.norm, method="scale")
> boxplot(gastro.norm) ## To see the efect of adjustment
> 
> ## To do VSN scale adjustment (from vsn package) use the command. Be
> ## carefull that this method adjust the variance along A values and not
> ## between chips!!
> gastro.norm = normScaleLimma(gastro.raw2, method="vsn")
> boxplot(gastro.norm) ## See the effect
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>